Preview

Georesources

Advanced search

The research of relationship between microbiological factors with the distribution of anomalous methane fields and the presence of gas hydrate deposits using the example of two water areas in the northern part of Japan Sea

https://doi.org/10.18599/grs.2025.3.3

Abstract

Our research focuses on the possibilities of using microorganisms as bioindicators in methane ecosystems in areas with gas hydrates (Area 1). We have conducted a study of the biodiversity of microorganisms and determined the physiological and biochemical properties of bacterial strains that can oxidize hydrocarbons isolated from the bottom sediments in the northern part of the Japan Sea for two areas: one with detected gas hydrates (Area 1) and one without the presence of gas hydrates (Area 2). Complex gas-geochemical, geological, and microbiological studies have been conducted in the waters of the northern Japan Sea, including the southern part of the Tatar Strait and the northern slope of Primorsky Krai. We used materials from marine expeditions: RV “Akademik Oparin” 54 (OP-54) in September–October 2017 and RV “Akademik M.A. Lavrentyev” 81 (LV-81) in May 2018. We used cultivation techniques to discover that members of the Nocardiaceae family from the Actinomycota phylum were associated with areas where gas hydrates had been detected. It was found that bacteria isolated from these areas were able to ferment a wider variety of carbohydrate substrates than those obtained from non-gas hydrate areas. A positive correlation was observed between the ability of these bacteria to break down carboxylic acids and their absence from gas hydrate-rich environments.

About the Authors

N. S. Syrbu
V.I. Il’ichev Pacific Oceanological Institute FEB RAS
Russian Federation

Nadezhda S. Syrbu – Cand. Sci. (Geology and Mineralogy, Head of the Laboratory for Integrated Research of Environment and Mineral Resources

43, Baltiyskaya st., Vladivostok, 690041



A. I. Eskova
V.I. Il’ichev Pacific Oceanological Institute FEB RAS
Russian Federation

Alena I. Eskova – Cand. Sci. (Biology), Senior Researcher of the Laboratory for Integrated Research of Environment and Mineral Resources

43, Baltiyskaya st., Vladivostok, 690041



A. A. Kholmogorov
V.I. Il’ichev Pacific Oceanological Institute FEB RAS
Russian Federation

Andrey O. Kholmogorov – Cand. Sci. (Geography), Senior Researcher of the Laboratory for Integrated Research of Environment and Mineral Resources

43, Baltiyskaya st., Vladivostok, 690041



A. A. Legkodimov
V.I. Il’ichev Pacific Oceanological Institute FEB RAS
Russian Federation

Aleksei A. Legkodimov – Junior Researcher, Laboratory for Integrated Research of Environment and Mineral Resources

43, Baltiyskaya st., Vladivostok, 690041



T. S. Yakimov
V.I. Il’ichev Pacific Oceanological Institute FEB RAS
Russian Federation

Timur S. Yakimov – Junior Researcher, Gas Geochemistry Laboratory

43, Baltiyskaya st., Vladivostok, 690041



A. L. Ponomareva
V.I. Il’ichev Pacific Oceanological Institute FEB RAS
Russian Federation

Anna L. Ponomoreva – Cand. Sci. (Biology), Senior Researcher, Laboratory for Integrated Research of Environment and Mineral Resources

43, Baltiyskaya st., Vladivostok, 690041



E. V. Maltseva
V.I. Il’ichev Pacific Oceanological Institute FEB RAS
Russian Federation

Elena V. Maltseva – Cand. Sci. (Geology and Mineralogy), Senior Researcher, Gas Geochemistry Laboratory

43, Baltiyskaya st., Vladivostok, 690041



References

1. Ashelford K.E., Chuzhanova N.A., Fry J.C., Jones A.J., Weinghtman A.J. (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol., 71(12), pp. 7724–7736. https://doi.org/10.1128/AEM.71.12.7724-7736.2005

2. Abrams M.A. (2017). Evaluation of Near-Surface Gases in Marine Sediments to Assess Subsurface Petroleum Gas Generation and Entrapment. Geosciences, 7. pp. 29–35. https://doi.org/10.3390/geosciences7020035

3. Baldanova K.O., Grigorov R.A., Eskova A.I., Kalgin V.Yu., Makseev D.S., Obzhirov A.I., Okulov A.K., Polonik N.S., Ponomareva A.L., Syrbu N.S., Shakirov R.B., Legkodimov A.A. (2022). Oil-oxidizing bacteria from bottom sediments of the northern part of the Japan Sea. Rospatent. Certificate No 2022621781. Date 20.07.2022. (In Russ.)

4. Bogatyrenko E. A., Kim A. V., Dunkai T. I., Ponomareva A.L., Eskova A.I., Sidorenko M.L., Okulov A.K. (2021). Taxonomic Diversity of Culturable Hydrocarbon-Oxidizing Bacteria in the Sea of Japan. Russian Journal of Marine Biology, 47(3). pp. 232–239. DOI 10.1134/S1063074021030032

5. Briggs B.R., Inagaki F., Morono Y., Futagami T., Huguet C., RosellMele A., et al. (2012). Bacterial dominance in subseafloor sediments characterized by methane hydrates. FEMS Microbiol. Ecol., 81, pp. 88–98. doi: 10.1111/j.1574-6941.2012.01311.x

6. Buzoleva L.S., Smirnova M.A., Bezverbnaya I.P. (2008). Biological features of oil degrading bacteria in coastal water areas with different types of pollution. Izvestiya TINRO, 155, pp. 210–218. (In Russ.)

7. Carrier V., Svenning M.M., Grundger F., Niemann H., Dessandier P.-A., Panieri G., et al. (2020). The impact of methane on microbial communities at marine Arctic gas hydrate bearing sediment. Front. Microbiol., 11:1932. doi: 10.3389/fmicb.2020.01932

8. Cho H., Hyun J.-H., You O.-R., Kim M., Kim S.-H., Choi D.-L., et al. (2017). Microbial community structure associated with biogeochemical processes in the sulfate–methane transition zone (SMTZ) of gas-hydratebearing sediment of the Ulleung Basin, East Sea. Geomicrobiol. J., 34, pp. 207–219. doi: 10.1080/01490451.2016.1159767

9. Ciobanu M.–C., Burgaud G., Dufresne A., Breuker A., Rédou V., Ben Maamar S., Gaboyer F. (2014). Microorganisms persist at record depths in the subseafloor of the Canterbury Basin. ISME J., 8(7), pp. 2352–2352. https://doi.org/10.1038/ismej.2014.110

10. Collett T., Johnson A., Knapp C., Boswell R. (2009). Natural Gas Hydrates: Energy Resource Potential and Associated Geologic Hazards; American Association of Petroleum Geologists: Tulsa, USA, p. 145.

11. Cui H., Su X., Chen F., Holland M., Yang S., Liang J., et al. (2019). Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea. Mar. Environ. Res., 144, pp. 230–239. doi: 10.1016/j.marenvres.2019.01.009

12. Cui H., Su X., Liang J., Chen F., Holland M., Yang S., et al. (2020). Microbial diversity in fracture and pore filling gas hydrate-bearing sediments at site GMGS2-16 in the Pearl River Mouth Basin, the South China Sea. Mar. Geol., 427, 106264. doi: 10.1016/j.margeo.2020.106264

13. Gresov A.I., Yatsuk A.V. (2021). Geological implications for gas saturation of bottom sediments in sedimentary basins in the southeastern sector of the east Siberian sea. Russian Geology and Geophysics, 62(2), pp. 157–172. DOI 10.2113/RGG20194075

14. Hovland M., Croker P.F., Martin M. (1994). Fault—Associated seabed mounds (carbonate knolls?) off western Ireland and north-west Australia. Mar. Pet. Geol., 11, pp. 232–246. https://doi.org/10.1016/0264-8172(94)90099-X

15. Jiao L., Su X., Wang Y., Jiang H., Zhang Y., and Chen F. (2015). Microbial diversity in the hydrate-containing and-free surface sediments in the Shenhu area, South China. Geosci. Front., 6, pp. 627–633. doi: 10.1016/j.gsf.2014.04.007

16. Jin Y.K., Shoji H., Obzhirov A., Baranov B. (2013) Operation Report of Sakhalin Slope Gas Hydrate Project 2012, R/V Akademik M.A. Lavrentyev Cruise 59; Korea Polar Research Institute: Incheon, Republic of Korea, p.163.

17. Katayama T., Yoshioka H., Kaneko M., Amo M., Fujii T., Takahashi H. A., et al. (2022). Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site. ISME J., 16, 1464–1472. doi: 10.1038/s41396-021-01175-7

18. Katayama T., Yoshioka H., Takahashi H. A., Amo M., Fujii T., and Sakata S. (2016). Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai trough. FEMS Microbiol. Ecol., 92. doi: 10.1093/femsec/fiw093

19. Kharakhinov V.V. (2010). Oil and gas geology of the Sakhalin region. Moscow: Nauchnyy mir, 276 p. (In Russ.)

20. Labinskaya A.S., Blinkova L.P., Eshchina A.S. (2005). Private medical microbiology with the technique of microbiological research. Moscow: Meditsina, 616 p. (In Russ.)

21. Lee J.-W., Kwon K. K., Aziz A., Oh H.-M., Kim W., Bahk J.-J., et al. (2013). Microbial community structures of methane hydrate-bearing sediments in the Ulleung Basin, East Sea of Korea. Mar. Pet. Geol., 47, pp. 136–146. doi: 10.1016/j.marpetgeo.2013.06.002

22. Liu S, Yu S, Lu X, Yang H, Li Y, Xu X, Lu H and Fang Y. (2022). Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea. Front. Microbiol., 13, 1032851. doi: 10.3389/fmicb.2022.1032851

23. Matsui K., Ishii N, Kawabata Z. (2003). Microbial interactions affecting the natural transformation of Bacillus subtilis in a modelaquatic ecosystem. FEMS Microbiol Ecol., 45(3). https://doi.org/10.1016/S0168-6496(03)00148-X

24. Marmur J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. Journal of Molecular Biology, 3, pp. 208–218. https://doi.org/10.1016/S0022-2836(61)80047-8

25. Mills H. J., Martinez R. J., Story S., Sobecky P. A. (2005). Characterization of microbial community structure in Gulf of Mexico gas hydrates: comparative analysis of DNA-and RNA-derived clone libraries. Appl. Environ. Microbiol., 71, pp. 3235–3247. doi: 10.1128/AEM.71.6.3235-3247.2005

26. Minami H., Jin Y.K., Baranov B., Nikolaeva N., Obzhirov A. (2016). Operation Report of Sakhalin Slope Gas Hydrate Project II, 2015, R/V Akademik M.A. Lavrentyev Cruise 70; Kitami Institute of Technology: Kitami, Japan, pp. 119.

27. Netrusov A.I., Egorova M.A., Zakharchuk L.M. (2005). Microbiology Workshop. Moscow: Akademiya, 608 p. (In Russ.)

28. Nechayuk A.E. (2017). The geological structure and dynamics of the formation of sedimentary basins of the Tatar Strait and western Sakhalin. Cand. geol. and min. sci. diss. Vladivostok, 99 p. (In Russ.)

29. Obzhirov A.I. (1993). Gas-geochemical fields of the bottom layer of seas and oceans. Moscow: Nauka, 139 p. (In Russ.)

30. Ponomareva A.L., Polonik N.S., Eskova A.I., Grigorov R.A., Khokkanen S.N., Syrbu N.S., Obzhirov A.I., Shakirov R.B., Legkodimov A.A. (2022). Degree of destruction and indices of biodegradation of hydrocarbons by strains isolated from the northern part of the Japan Sea under aerobic and anaerobic conditions. Rospatent. Certificate No 2022623218. 05.12.2022. (In Russ.)

31. Repina (Smirnova) M.A. (2009). Petro-carbohydrate-oxidizing microorganisms of coastal waters of the south of Sakhalin Island. Cand. biol. sci. diss. Vladivostok, 149 p. (In Russ.)

32. Romanenko L.A., Schumann P., Zhukova N.V., Rohde M., Mikhailov V.V., Stackebrandt, E. (2003). Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments. Int. J. Syst. Evol. Microbiol., 53, pp. 1885–1888. https://doi.org/10.1099/ijs.0.02774-0

33. Romanenko LA, Lysenko AM, Rohde M, Mikhailov VV, Stackebrandt E. (2004). Psychrobacter maritimus sp. nov. and Psychrobacter arenosus sp. nov., isolated from coastal sea ice and sediments of the Sea of Japan. Int J Syst Evol Microbiol., 54(Pt 5), pp. 1741–1745. doi: 10.1099/ijs.0.63096-0

34. Ryu B.-J., Collett T. S., Riedel M., Kim G. Y., Chun J.-H., Bahk J.-J., et al. (2013). Scientific results of the second gas hydrate drilling expedition in the Ulleung Basin (UBGH2). Mar. Pet. Geol., 47, pp. 1–20. doi: 10.1016/j.marpetgeo.2013.07.007

35. Schoell M. (1988). Multiple origins of methane in the earth. Chem. Geol., 71, pp. 1–10. doi: 10.1016/0009-2541(88)90101-5

36. Seki T., Matsumoto A., Omura S., Takahashi Y. (2015). Distribution and isolation of strains belonging to the order Solirubrobacterales. The Journal of Antibiotics, 68, pp. 763–766. https://doi.org/10.1038/ja.2015.67

37. Shakirov R.B., Sorochinskaya A.V., Yatsuk A.V., Aksenov K.I., Karabtsov A.A., Vovna V.I., Osmushko I.S., Korochentsev V.V. (2020). It hiccups in the methane anomaly zone on the continental slope of the Sea of Japan. Vestnik KRAUNTs. Nauki o Zemle, 2(46), pp. 72–84. (In Russ.)

38. Shakirov R.B., Syrbu N.S., Obzhirov A.I. (2016). Distribution of helium and hydrogen in sediments and water on the Sakhalin slope. Lithol. Miner. Resour., 51, pp. 61–73. https://doi.org/10.1134/S0024490216010065

39. Shakirov R.B., Yatsuk A.V., Sorochinskaya A.V., Aksentov K.I., Makseev D.S. (2023). Gas Geochemical Anomalies in Bottom Sediments of the Tatar Trough (Sea of Japan). Doklady Earth Sciences, 513. DOI 10.1134/S1028334X23602171

40. Shaposhnikov G.N., Alexandrov G.P., Egorov S.V. et al. (1995). State Geological Map of the Russian Federation. Scale 1:1,000,000 (new series). Sheet L-(54), (55); K-(55) — Yuzhno-Sakhalinsk. An explanatory note. St. Petersburg: VSEGEI Cartographic Factory, 146 p. (In Russ.)

41. Shoji H., Jin Y.K., Baranov B., Nikolaeva N., Obzhirov A. (2014). Operation Report of Sakhalin Slope Gas Hydrate Project II, 2013, R/V Akademik M.A. Lavrentyev Cruise 62; Environmental and Energy Resources Research Center, Kitami University: Kitami, Japan, p. 110.

42. Starobinets I.S., Petukhov A.V., Zubayraev S.L. et al. (1993). Fundamentals of the theory of geochemical fields of hydrocarbon accumulations. Moscow: Nedra, 332 p. (In Russ.)

43. Syrbu N., Kholmogorov A., Stepochkin I., Lobanov V., Shkorba S. (2024). Formation of Abnormal Gas-Geochemical Fields and Dissolved Gases Transport at the Shallow Northeastern Shelf of Sakhalin Island in Warm Season: Expedition Data and Remote Sensing. Water, 16, 1434. https://doi.org/10.3390/w16101434

44. Syrbu N.S., Snyder G.T., Shakirov R.B., Kholmogorov A.O., Zharkov R.V., Tsunogai U. (2022).Geochemical distribution of helium, hydrogen, carbon dioxide, and methane in Sakhalin Island mud volcanoes, hot springs, and cold seeps. J. Volcanol. Geotherm. Res., 431, 107667. https://doi.org/10.1016/j.jvolgeores.2022.107667

45. Walsh E. A., Kirkpatrick B., Pockalny R. (2016). Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment. Applied and Environmental Microbiology, 8 (16), pp. 4994–4999. https://doi.org/10.1128/AEM.00809-16

46. Whiticar M. J. (1999). Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane. Chem. Geol., 161, pp. 291–314. doi: 10.1016/S0009-2541(99)00092-3

47. Wiessenburg D.A., Guinasso N.L. (1979). Equilibrium solubility of methane, carbon dioxide, and hydrogen in water and sea water. J. Chem. Eng. Data, 24(4), pp. 356–360. https://doi.org/10.1021/je60083a006

48. Wuebbles D. J., Hayhoe K. (2002). Atmospheric methane and global change. Earth Sci. Rev., 57, pp. 177–210. doi: 10.1016/S0012-8252(01)00062-9

49. Yamamoto S., Alcauskas J.B., Crozier T.E. (1976). Solubility of methane in distilled water and seawater. J.Chem. Engineering Data, 21(1), pp. 78–80. https://doi.org/10.1021/je60068a029

50. Yanagawa K., Kouduka M., Nakamura Y., Hachikubo A., Tomaru H., Suzuki Y. (2014). Distinct microbial communities thriving in gas hydrateassociated sediments from the eastern Japan Sea. J. Asian Earth Sci., 90, pp. 243–249. doi: 10.1016/j.jseaes.2013.10.019

51. Yakimov T.S., Shakirov R.B., Syrbu N.S., Kholmogorov A.O., Sorochinskaya A.V. (2023). Manifestations of authigenic mineralization along the continental slope of the Sea of Japan and in the Tatar Strait (materials of Cruise 61 on r/v Akademik Oparin). Tikhookeanskaya geologiya, 42(4), pp. 101–114. (In Russ.) DOI: 10.30911/0207-4028-2023-42-4-101-114

52. Zharov A.E., Kirillova G.L., Margulis L.S., Chuyko L.S., et al. (2004). Geology, geodynamics and oil and gas potential of sedimentary basins of the Tatar Strait. Vladivostok: DVO RAN, 220 p. (In Russ.)

53. Zhemchugova T.A. (2013). Oil and gas potential of Cenozoic deposits in the central part of the Tatar Strait. Moscow University Bulletin. Series 4. Geology, 2, pp. 69–75. (In Russ.)

54.


Review

For citations:


Syrbu N.S., Eskova A.I., Kholmogorov A.A., Legkodimov A.A., Yakimov T.S., Ponomareva A.L., Maltseva E.V. The research of relationship between microbiological factors with the distribution of anomalous methane fields and the presence of gas hydrate deposits using the example of two water areas in the northern part of Japan Sea. Georesursy = Georesources. 2025;27(3):36-50. (In Russ.) https://doi.org/10.18599/grs.2025.3.3

Views: 17


Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.


ISSN 1608-5043 (Print)
ISSN 1608-5078 (Online)